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Series GSE142182 Query DataSets for GSE142182
Status Public on Jan 09, 2020
Title Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [RNA-Seq]
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Deletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that are generally more sensitive to rapid TFIID depletion. However, transcription of these “coactivator-redundant” genes is strongly affected by rapid depletion of both factors, showing the overlapping functions of TFIID and SAGA at this gene set. We suggest that this overlapping function is linked to TBP-DNA recruitment. The remaining 87% of expressed genes that we term “TFIID-dependent” are highly sensitive to rapid TFIID depletion and insensitive to rapid SAGA depletion. Genome-wide mapping of SAGA and TFIID found binding of both factors at many genes independent of gene class. DNA analysis suggests that the distinction between the gene classes is due to multiple components rather than any single regulatory factor or promoter sequence motif.
 
Overall design Newly synthesized RNAs were labeled with 4-thioU, purified and analyzed with RNA-seq. Depletion of TFIID and/or SAGA subunits was achieved either thorugh targeted degradation (auxin-degron system) or SAGA subunits deletion. Corresponding control and treatment sample files are labeled DMSO and 3IAA, respectively. For SAGA subunit deletion strain BY4705 was used to construct spt20 and spt7 deletion strains and strain SHY565 was used to construct spt3 deletion strain. All experiments were done in two (A,B) or three replicates (A,B,C).
 
Contributor(s) Donczew R, Warfield L, Pacheco D, Erijman A, Hahn S
Citation(s) 31913117
Submission date Dec 17, 2019
Last update date Apr 09, 2020
Contact name Rafal Donczew
E-mail(s) Rafal-donczew@omrf.org
Organization name Oklahoma Medical Research Foundation
Department Cell Cycle and Cancer Biology
Lab Hahn Lab
Street address 825 NE 13th St
City Oklahoma City
State/province OK
ZIP/Postal code 73104
Country USA
 
Platforms (1)
GPL17342 Illumina HiSeq 2500 (Saccharomyces cerevisiae)
Samples (11)
GSM4222243 WT_4705_A
GSM4222244 WT_4705_B
GSM4222245 WT_4TU_input
This SubSeries is part of SuperSeries:
GSE142122 Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA
Relations
BioProject PRJNA596180
SRA SRP237925

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE142182_RAW.tar 480.0 Kb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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